Graham McVicker

Frederick B. Rentschler Developmental Chair
Assistant Professor
Laboratory of Genetics
Integrative Biology Laboratory

Salk Institute for Biological Studies - Publications

all Publications


Martin, R.L., Maiorano, J., Beitel, G.J., Marko, J.F., McVicker, G., Fondufe-Mittendorf, Y.N. A comparison of nucleosome organization in Drosophila cell lines. (2017) PLoS ONE. 12(6):e0178590. DOI: 10.1371/journal.pone.0178590

+ expand abstract


Elyashiv, E., Sattath, S., Hu, T.T., Strutsovsky, A., McVicker, G., Andolfatto, P., Coop, G., Sella, G. A Genomic Map of the Effects of Linked Selection in Drosophila. (2016) PLoS Genet. 12(8):e1006130. DOI: 10.1371/journal.pgen.1006130

+ expand abstract


van de Geijn, B.*, McVicker, G.*, Gilad, Y., Pritchard, J.K. WASP: allele-specific software for robust molecular quantitative trait locus discovery. (2015) Nat. Methods. 12(11):1061-3. DOI: 10.1038/nmeth.3582

+ expand abstract


Banovich, N.E., Lan, X., McVicker, G., van de Geijn, B., Degner, J.F., Blischak, J.D., Roux, J., Pritchard, J.K., Gilad, Y. Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. (2014) PLoS Genet. 10(9):e1004663. DOI: 10.1371/journal.pgen.1004663

+ expand abstract


Nalabothula, N.*, McVicker, G.*, Maiorano, J., Martin, R., Pritchard, J.K., Fondufe-Mittendorf, Y.N. The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation. (2014) BMC Genomics. 15:92. DOI: 10.1186/1471-2164-15-92

+ expand abstract


Raj, A., McVicker, G. The genome shows its sensitive side. (2014) Nat. Methods. 11(1):39-40. DOI: 10.1038/nmeth.2770


McVicker, G.*, van de Geijn, B.*, Degner, J.F., Cain, C.E., Banovich, N.E., Raj, A., Lewellen, N., Myrthil, M., Gilad, Y., Pritchard, J.K. Identification of genetic variants that affect histone modifications in human cells. (2013) Science. 342(6159):747-9. DOI: 10.1126/science.1242429

+ expand abstract


Gaffney, D.J.*, McVicker, G.*, Pai, A.A., Fondufe-Mittendorf, Y.N., Lewellen, N., Michelini, K., Widom, J., Gilad, Y., Pritchard, J.K. Controls of nucleosome positioning in the human genome. (2012) PLoS Genet. 8(11):e1003036. DOI: 10.1371/journal.pgen.1003036

+ expand abstract


George, R.D., McVicker, G., Diederich, R., Ng, S.B., MacKenzie, A.P., Swanson, W.J., Shendure, J., Thomas, J.H. Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection. (2011) Genome Res. 21(10):1686-94. DOI: 10.1101/gr.121327.111

+ expand abstract


D'Souza, C.A., Kronstad, J.W., Taylor, G., Warren, R., Yuen, M., Hu, G., Jung, W.H., Sham, A., Kidd, S.E., Tangen, K., Lee, N., Zeilmaker, T., Sawkins, J., McVicker, G., Shah, S., Gnerre, S., Griggs, A., Zeng, Q., Bartlett, K., Li, W., Wang, X., Heitman, J., Stajich, J.E., Fraser, J.A., Meyer, W., Carter, D., Schein, J., Krzywinski, M., Kwon-Chung, K.J., Varma, A., Wang, J., Brunham, R., Fyfe, M., Ouellette, B.F., Siddiqui, A., Marra, M., Jones, S., Holt, R., Birren, B.W., Galagan, J.E., Cuomo, C.A. Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts. (2011) MBio. 2(1):e00342-10. DOI: 10.1128/mBio.00342-10

+ expand abstract


McVicker, G., Green, P. Genomic signatures of germline gene expression. (2010) Genome Res. 20(11):1503-11. DOI: 10.1101/gr.106666.110

+ expand abstract


McVicker, G., Gordon, D., Davis, C., Green, P. Widespread genomic signatures of natural selection in hominid evolution. (2009) PLoS Genet. 5(5):e1000471. DOI: 10.1371/journal.pgen.1000471

+ expand abstract


Hubbard, T., Andrews, D., Caccamo, M., Cameron, G., Chen, Y., Clamp, M., Clarke, L., Coates, G., Cox, T., Cunningham, F., Curwen, V., Cutts, T., Down, T., Durbin, R., Fernandez-Suarez, X.M., Gilbert, J., Hammond, M., Herrero, J., Hotz, H., Howe, K., Iyer, V., Jekosch, K., Kahari, A., Kasprzyk, A., Keefe, D., Keenan, S., Kokocinsci, F., London, D., Longden, I., McVicker, G., Melsopp, C., Meidl, P., Potter, S., Proctor, G., Rae, M., Rios, D., Schuster, M., Searle, S., Severin, J., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Trevanion, S., Ureta-Vidal, A., Vogel, J., White, S., Woodwark, C., Birney, E. Ensembl 2005. (2005) Nucleic Acids Res. 33(Database i):D447-53. DOI: 10.1093/nar/gki138

+ expand abstract


Stabenau, A., McVicker, G., Melsopp, C., Proctor, G., Clamp, M., Birney, E. The Ensembl core software libraries. (2004) Genome Res. 14(5):929-33. DOI: 10.1101/gr.1857204

+ expand abstract


Birney, E., Andrews, T.D., Bevan, P., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cuff, J., Curwen, V., Cutts, T., Down, T., Eyras, E., Fernandez-Suarez, X.M., Gane, P., Gibbins, B., Gilbert, J., Hammond, M., Hotz, H.R., Iyer, V., Jekosch, K., Kahari, A., Kasprzyk, A., Keefe, D., Keenan, S., Lehvaslaiho, H., McVicker, G., Melsopp, C., Meidl, P., Mongin, E., Pettett, R., Potter, S., Proctor, G., Rae, M., Searle, S., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Ureta-Vidal, A., Woodwark, K.C., Cameron, G., Durbin, R., Cox, A., Hubbard, T., Clamp, M. An overview of Ensembl. (2004) Genome Res. 14(5):925-8. DOI: 10.1101/gr.1860604

+ expand abstract


Birney, E., Andrews, D., Bevan, P., Caccamo, M., Cameron, G., Chen, Y., Clarke, L., Coates, G., Cox, T., Cuff, J., Curwen, V., Cutts, T., Down, T., Durbin, R., Eyras, E., Fernandez-Suarez, X.M., Gane, P., Gibbins, B., Gilbert, J., Hammond, M., Hotz, H., Iyer, V., Kahari, A., Jekosch, K., Kasprzyk, A., Keefe, D., Keenan, S., Lehvaslaiho, H., McVicker, G., Melsopp, C., Meidl, P., Mongin, E., Pettett, R., Potter, S., Proctor, G., Rae, M., Searle, S., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Ureta-Vidal, A., Woodwark, C., Clamp, M., Hubbard, T. Ensembl 2004. (2004) Nucleic Acids Res. 32(Database i):D468-70. DOI: 10.1093/nar/gkh038

+ expand abstract


Shah, S.P., McVicker, G.P., Mackworth, A.K., Rogic, S., Ouellette, B.F. GeneComber: combining outputs of gene prediction programs for improved results. (2003) Bioinformatics. 19(10):1296-7.

+ expand abstract


Education

PhD Genome Sciences, University of Washington
BS Computer Science, University of British Columbia


Awards & Honors

  • 2009 Society for Molecular Biology and Evolution Graduate Student Travel Award
  • 2005 Natural Science and Engineering Research Council Post Graduate Scholarship
  • 1997 University of British Columbia Outstanding Student Initiative Scholarship

Profile